Positioning unconnected bones in pose mode using cursor
All your bones need to be positioned correctly in Edit mode. In Edit mode you will build the basic/rest pose of the character. All the changes you will make in Pose mode are only for animations purpose (or to create static particular poses) and won't affect the bone positions in Edit mode. So if the bone aligned to an object is supposed to be the rest pose, you have to do it in Edit mode, if this is supposed to be an animation pose, do it in Pose mode.